/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | PartitionReads.java | 112 qfin1=parser.qfin1; in PartitionReads() 133 if(qfin1!=null && qfin2==null && qfin1.indexOf('#')>-1 && !new File(qfin1).exists()){ in PartitionReads() 134 qfin2=qfin1.replace("#", "2"); in PartitionReads() 135 qfin1=qfin1.replace("#", "1"); in PartitionReads() 242 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 373 private String qfin1=null; field in PartitionReads
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H A D | BBQC.java | 98 qfin1=b; in BBQC() 378 …final String in1s=stripDirs(in1), in2s=stripDirs(in2), qfin1s=stripDirs(qfin1), qfin2s=stripDirs(q… in process() 381 ktrim(in1, in2, out1s, out2s, qfin1, qfin2, qfout1s, qfout2s, trimPrefix); in process() 495 if(qfin1!=null){argList.add("qfin1="+qfin1);} in ktrim() 556 …private void filter(String in1, String in2, String out1, String out2, String qfin1, String qfin2, … in filter() argument 588 …if(qfin1!=null){argList.add("qfin1="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in filter() 655 …private void dehumanize(String in1, String in2, String out1, String out2, String qfin1, String qfi… in dehumanize() argument 701 …if(qfin1!=null){argList.add("qfin1="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in dehumanize() 737 …private void normalize(String in1, String in2, String out1, String out2, String qfin1, String qfin… in normalize() argument 788 …if(qfin1!=null){argList.add("qfin1="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in normalize() [all …]
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H A D | AdjustHomopolymers.java | 89 qfin1=parser.qfin1; in AdjustHomopolymers() 183 qfin1=Tools.fixExtension(qfin1); in fixExtensions() 283 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris() 459 private String qfin1=null; field in AdjustHomopolymers
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H A D | KeepBestCopy.java | 108 qfin1=parser.qfin1; in KeepBestCopy() 139 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in makeCris() 258 private String qfin1=null; field in KeepBestCopy
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H A D | FungalRelease.java | 143 qfin1 = parser.qfin1; in FungalRelease() 200 cris = ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in process() 433 private String qfin1 = null; field in FungalRelease
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H A D | KmerCountMulti.java | 137 qfin1=parser.qfin1; in KmerCountMulti() 216 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 466 private String qfin1=null;
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H A D | MakeChimeras.java | 96 qfin1=parser.qfin1; in MakeChimeras() 130 cris=ConcurrentReadInputStream.getReadInputStream(readsIn, false, ffin1, null, qfin1, null); in process() 335 private String qfin1=null; field in MakeChimeras
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H A D | ReplaceHeaders.java | 113 qfin1=parser.qfin1; in ReplaceHeaders() 219 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 401 private String qfin1=null; field in ReplaceHeaders
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H A D | KExpand.java | 87 qfin1=parser.qfin1; in KExpand() 246 qfin1=Tools.fixExtension(qfin1); in fixExtensions() 373 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris() 787 private String qfin1=null; field in KExpand
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H A D | TranslateSixFrames.java | 123 qfin1=parser.qfin1; in TranslateSixFrames() 197 …cris=ConcurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, … in process() 368 private String qfin1=null; field in TranslateSixFrames
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H A D | CorrelateBarcodes.java | 108 qfin1=parser.qfin1; in CorrelateBarcodes() 180 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 382 private String qfin1=null; field in CorrelateBarcodes
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H A D | CountBarcodes.java | 128 qfin1=parser.qfin1; in CountBarcodes() 202 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 375 private String qfin1=null; field in CountBarcodes
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H A D | MergeBarcodes.java | 111 qfin1=parser.qfin1; in MergeBarcodes() 286 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in mergeWithMap() 404 private String qfin1=null; field in MergeBarcodes
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/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | AllToAll.java | 81 qfin1=parser.qfin1; in AllToAll() 144 qfin1=Tools.fixExtension(qfin1); in fixExtensions() 200 …reads=ConcurrentReadInputStream.getReads(maxReads, true, ffin1, null, qfin1, null); //TODO: Note … in process() 393 private String qfin1=null;
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/dports/biology/bbmap/bbmap/current/template/ |
H A D | A_Sample.java | 85 qfin1=parser.qfin1; in A_Sample() 175 qfin1=Tools.fixExtension(qfin1); in fixExtensions() 275 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris() 402 private String qfin1=null; field in A_Sample
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H A D | A_SampleMT.java | 85 qfin1=parser.qfin1; in A_SampleMT() 178 qfin1=Tools.fixExtension(qfin1); in fixExtensions() 288 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); 494 private String qfin1=null;
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H A D | A_Sample_Unpaired.java | 102 qfin1=parser.qfin1; in A_Sample_Unpaired() 135 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in process() 222 private String qfin1=null; field in A_Sample_Unpaired
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H A D | BBTool_ST.java | 103 qfin1=parser.qfin1; in BBTool_ST() 268 if(!Tools.testForDuplicateFiles(true, in1, in2, qfin1, qfin2, out1, out2, qfout1, qfout2)){ in startup() 276 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in startup() 409 protected String qfin1=null; field in BBTool_ST
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/dports/biology/bbmap/bbmap/current/prok/ |
H A D | SplitRibo.java | 84 qfin1=parser.qfin1; in SplitRibo() 174 qfin1=Tools.fixExtension(qfin1); in fixExtensions() 300 …Stream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); 562 private String qfin1=null;
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H A D | RiboMaker.java | 91 qfin1=parser.qfin1; in RiboMaker() 186 qfin1=Tools.fixExtension(qfin1); in fixExtensions() 372 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); 626 private String qfin1=null;
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/dports/biology/bbmap/bbmap/current/tax/ |
H A D | FilterByTaxa.java | 115 qfin1=parser.qfin1; in FilterByTaxa() 214 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 368 private String qfin1=null; field in FilterByTaxa
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/dports/biology/bbmap/bbmap/current/driver/ |
H A D | LoadReads.java | 113 qfin1=parser.qfin1; in LoadReads() 177 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 388 private String qfin1=null; field in LoadReads
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/dports/biology/bbmap/bbmap/current/hiseq/ |
H A D | PlotFlowCell.java | 133 qfin1=parser.qfin1; in PlotFlowCell() 234 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in loadKmers() 259 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in fillTiles() 516 private String qfin1=null; field in PlotFlowCell
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/dports/biology/bbmap/bbmap/current/sort/ |
H A D | Shuffle.java | 139 qfin1=parser.qfin1; in Shuffle() 213 …cris=ConcurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, … in process() 384 private String qfin1=null; field in Shuffle
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | KmerLimit.java | 150 qfin1=parser.qfin1; in KmerLimit() 255 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 579 private String qfin1=null; field in KmerLimit
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